Exploring Cell-Types in UNS data

The cell annotated as UNS by Cano-Gamez et al. were T cells that were neither stimulated by cytokines nor had an activated TCR. To facilitate the analysis, these cells were analyzed seperatly.

Loading the necessary libraries

Load preprocessed scRNA-seq data
See notebook "Data preprocessing" for this analysis part

Dimension Reduction

PCA

Separate the data in UNS and stimulated

Plot PCA

UMAP

Louvain Clustering

The Louvain algorthim was chosen for clustering as it was used by Cano-Gamez et al.

! Caution: Rerunning your code will change the cluster composition due to randomness of the algorthim !

Explore the composition of the clusters

Most clusters can be clearly assigned to one particluar cell type. Only cluster 5 seems to conist of a mixture of memory and naive cells.

Rank genes

Mostly ribosomal proteins. No indication of cell types

Cluster Annotation

Annotate naive cells

Used marker genes

The marker genes from literature are based on the following website: https://www.biocompare.com/Editorial-Articles/569888-A-Guide-to-T-Cell-Markers/

T cell type / differentiation state Marker genes mentioned in Cano-Gamez et al.
central memory T cells (Tcm) PASK
effector memory T cells (Tem) IL7R, KLRB1, TNFSF13B
terminally differentiated effector cells (TEMRA) CCL4, GZMA
natural T regulatory cells (nTreg) FOXP3, CTLA4
T cell type / differentiation state Marker genes literature
T naive (Tn) CCR7
central memory T cells (Tcm) FAS, IL2RB, PRDM1
effector memory T cells (Tem) CXCR3, ITGAL, CCR5, TBX21

Map marker genes on clusters

TEMRA

-> markers clearly expressed in cluster 5

nTreg

-> marker genes expressed in cluster 6

Tn

-> marker genes mostly expressed in cluster 0, 2 and 7

Tcm

-> Tcm marker expression present in cluster 3 and 1

TEM literature

TEM paper

-> Tem cells can be assinged to cluster 4

Add annotation to AnnData

Create annotation

Add annotation to data

Plotting

Similar annotation as by Cano-Gamez et al., see: https://cytokines.cellgeni.sanger.ac.uk/resting

Save data